id: A0A9L0I7X9 gene_symbol: IRF9 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:9793 label: Equus asinus description: IRF9 (interferon regulatory factor 9, ISGF3-gamma, p48) is the DNA-binding subunit of the interferon-stimulated gene factor 3 (ISGF3) transcription factor. After type I interferon (IFN-alpha/beta) activates the JAK kinases TYK2 and JAK1, IRF9 associates through its C-terminal IRF-association domain with tyrosine-phosphorylated STAT2 and STAT1, and the ISGF3 complex accumulates in the nucleus, where the N-terminal tryptophan-pentad DNA-binding domain of IRF9 recognizes the interferon-stimulated response element (ISRE) and drives RNA polymerase II transcription of interferon-stimulated genes, establishing an antiviral state. The donkey protein belongs to the IRF9 subfamily of the interferon regulatory factor family, conserves the DNA-binding domain, including all five pentad tryptophans, and the IRF-association domain, and carries a 33-residue C-terminal extension relative to human IRF9. existing_annotations: - term: id: GO:0000976 label: transcription cis-regulatory region binding evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: enables supporting_entities: - ARBA:ARBA00028970 - InterPro:IPR001346 review: summary: IRF9 binds the ISRE in promoters of interferon-stimulated genes; true, but entailed by the more specific RNA polymerase II cis-regulatory sequence-specific DNA binding term accepted in this review. action: TOO_GENERAL reason: The claim is correct. GO:0000978 (RNA polymerase II cis-regulatory region sequence-specific DNA binding), accepted below on the basis of the conserved IRF DNA-binding domain and human IRF9 ISRE-binding data, is an is_a descendant of this term (verified in OLS), so this row adds no information. supported_by: - reference_id: PMID:1630447 supporting_text: ISGF3 gamma serves as the DNA recognition subunit - reference_id: file:EQUAS/IRF9/IRF9-bioinformatics/dbd_check.md supporting_text: '98 of 108 residues identical in donkey A0A9L0I7X9.' - term: id: GO:0000978 label: RNA polymerase II cis-regulatory region sequence-specific DNA binding evidence_type: IEA original_reference_id: GO_REF:0000118 qualifier: enables supporting_entities: - PANTHER:PTN008986835 review: summary: IRF9 recognizes ISRE sequences in RNA polymerase II promoters of interferon-stimulated genes. action: ACCEPT reason: The TreeGrafter transfer places the donkey protein in PANTHER subfamily PTHR11949:SF26 (IRF9), the same subfamily as human Q00978 and mouse Q61179, so the subfamily-level DNA-binding function applies. Human ISGF3-gamma binds DNA sequence-specifically in vitro, and IRF9-deficient human cells lose ISRE binding. The donkey DNA-binding domain is 91% identical to human with all five pentad tryptophans conserved. supported_by: - reference_id: PMID:1630447 supporting_text: ISGF3 gamma translated in vitro from recombinant clones bound DNA with a specificity indistinguishable from that of ISGF3 gamma purified from HeLa cells - reference_id: PMID:30143481 supporting_text: were not able to form a functional ISGF3 complex following IFN-α2b stimulation, as evidenced by abolished ISRE binding in vitro - reference_id: file:EQUAS/IRF9/IRF9-uniprot.txt record_section: ["DR:PANTHER"] supporting_text: PTHR11949:SF26; INTERFERON REGULATORY FACTOR 9 - reference_id: file:EQUAS/IRF9/IRF9-bioinformatics/dbd_check.md supporting_text: 'human W80 -> donkey W80' - term: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific evidence_type: IEA original_reference_id: GO_REF:0000118 qualifier: enables supporting_entities: - PANTHER:PTN008986835 review: summary: IRF9 is a sequence-specific RNA polymerase II transcription factor acting within ISGF3. action: ACCEPT reason: Core molecular function, transferred within PANTHER subfamily PTHR11949:SF26. IRF9 supplies the sequence-specific DNA recognition of ISGF3; loss of IRF9 abolishes ISRE-driven reporter transcription in human cells, and the donkey protein retains the DNA-binding and IRF-association domains. supported_by: - reference_id: PMID:30143481 supporting_text: U2A cells transfected with IRF9-Δex7 exhibited abolished luciferase transcription when luciferase production was driven from an IFN-stimulated response element (ISRE) promoter - reference_id: PMID:1630447 supporting_text: ISGF3 gamma serves as the DNA recognition subunit - term: id: GO:0002376 label: immune system process evidence_type: IEA original_reference_id: GO_REF:0000118 qualifier: involved_in supporting_entities: - PANTHER:PTN008986835 review: summary: True but uninformative; IRF9's immune role is specifically type I interferon signalling. action: MODIFY reason: The family-level PAINT term is correct for IRF9, but the specific, well-established process is type I interferon-mediated signalling, in which IRF9 is the DNA-binding component of ISGF3 that carries the signal to interferon-stimulated gene promoters. IRF9-deficient human cells fail to form ISGF3 in response to IFN-alpha2b. This replacement is the transducing step IRF9 itself performs, not a downstream organismal phenotype. proposed_replacement_terms: - id: GO:0060337 label: type I interferon-mediated signaling pathway supported_by: - reference_id: PMID:30143481 supporting_text: Her cells activate gamma-activated factor (GAF) STAT1 homodimers but not IFN-stimulated gene factor 3 (ISGF3) trimers (STAT1/STAT2/IRF9) in response to IFN-α2b. - reference_id: file:EQUAS/IRF9/IRF9-bioinformatics/human_Q00978-uniprot.txt record_section: ["CC:FUNCTION"] supporting_text: It mediates signaling by type I IFNs (IFN-alpha and IFN-beta). - term: id: GO:0003677 label: DNA binding evidence_type: IEA original_reference_id: GO_REF:0000104 qualifier: enables supporting_entities: - UniRule:UR000400841 review: summary: True but entailed by the sequence-specific RNA polymerase II cis-regulatory DNA-binding annotation. action: TOO_GENERAL reason: IRF9 binds DNA, but RNA polymerase II cis-regulatory region sequence-specific DNA binding, accepted in this review, is a descendant of this term (verified in OLS) and already entails it. supported_by: - reference_id: file:EQUAS/IRF9/IRF9-bioinformatics/dbd_check.md supporting_text: '98 of 108 residues identical in donkey A0A9L0I7X9.' - term: id: GO:0003700 label: DNA-binding transcription factor activity evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: enables supporting_entities: - ARBA:ARBA00028295 - InterPro:IPR019471 - InterPro:IPR019817 review: summary: Correct, but the parent of the RNA polymerase II-specific transcription factor activity accepted in this review. action: TOO_GENERAL reason: The claim is true. GO:0000981 (DNA-binding transcription factor activity, RNA polymerase II-specific), accepted above as the core function, is an is_a descendant of this term (verified in OLS), so this row is entailed. supported_by: - reference_id: PMID:1630447 supporting_text: ISGF3 gamma serves as the DNA recognition subunit - term: id: GO:0005634 label: nucleus evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: located_in supporting_entities: - UniProtKB-SubCell:SL-0191 - PANTHER:PTN008986835 - UniRule:UR000400841 review: summary: ISGF3 containing IRF9 acts in the nucleus; IRF9 shuttles and accumulates there upon interferon stimulation. action: ACCEPT reason: Nuclear localization of human IRF9 is shown by fractionation, IRF9 is regulated by nucleocytoplasmic redistribution, and IRF9 acts in the nucleus as the DNA-binding subunit of ISGF3. The nucleus is where the core activity is executed. supported_by: - reference_id: PMID:30143481 supporting_text: a small amount of IRF9 was visible in the nucleus even under basal conditions - reference_id: PMID:11846981 supporting_text: IRF-3 and IRF-9 are examples of IRFs that are regulated by cellular redistribution. - term: id: GO:0006351 label: DNA-templated transcription evidence_type: IEA original_reference_id: GO_REF:0000104 qualifier: involved_in supporting_entities: - UniRule:UR000400841 review: summary: IRF9 regulates transcription; it does not perform it. action: MARK_AS_OVER_ANNOTATED reason: RNA polymerase II executes transcription; a sequence-specific transcription factor is properly described by its DNA-binding transcription factor activity and by positive regulation of transcription by RNA polymerase II, both accepted here. The UniRule keyword mapping to transcription itself overstates IRF9's role. supported_by: - reference_id: PMID:1630447 supporting_text: Alpha interferon stimulates transcription by converting the positive transcriptional regulator ISGF3 from a latent to an active form. - term: id: GO:0006355 label: regulation of DNA-templated transcription evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: involved_in supporting_entities: - InterPro:IPR019471 - InterPro:IPR019817 - UniRule:UR000400841 review: summary: Correct; IRF9 regulates transcription of interferon-stimulated genes, but this is entailed by positive regulation of transcription by RNA polymerase II. action: TOO_GENERAL reason: The claim is true but uninformative here. GO:0045944 (positive regulation of transcription by RNA polymerase II), accepted below, is a descendant of this term (verified in OLS). supported_by: - reference_id: PMID:30143481 supporting_text: U2A cells transfected with IRF9-Δex7 exhibited abolished luciferase transcription when luciferase production was driven from an IFN-stimulated response element (ISRE) promoter - term: id: GO:0006357 label: regulation of transcription by RNA polymerase II evidence_type: IEA original_reference_id: GO_REF:0000118 qualifier: involved_in supporting_entities: - PANTHER:PTN008986835 review: summary: Correct; IRF9 regulates RNA polymerase II transcription of interferon-stimulated genes, but this is entailed by the positive-regulation child accepted in this review. action: TOO_GENERAL reason: The PAINT node assertion is sound for the IRF9 subfamily, but IRF9 within ISGF3 is an activator, and GO:0045944 (positive regulation of transcription by RNA polymerase II), accepted below, is a descendant of this term (verified in OLS). supported_by: - reference_id: PMID:1630447 supporting_text: Alpha interferon stimulates transcription by converting the positive transcriptional regulator ISGF3 from a latent to an active form. - term: id: GO:0045944 label: positive regulation of transcription by RNA polymerase II evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: involved_in supporting_entities: - ARBA:ARBA00027996 review: summary: ISGF3 activates RNA polymerase II transcription of interferon-stimulated genes. action: ACCEPT reason: Activation of interferon-stimulated genes through the ISRE is the output of IRF9 activity. The ARBA source is not itself evidence, but human IRF9 is required for ISRE-driven transcription, and the donkey protein sits in the same PANTHER subfamily (PTHR11949:SF26) with conserved DNA-binding and IRF-association domains. supported_by: - reference_id: PMID:30143481 supporting_text: U2A cells transfected with IRF9-Δex7 exhibited abolished luciferase transcription when luciferase production was driven from an IFN-stimulated response element (ISRE) promoter - reference_id: PMID:1630447 supporting_text: Alpha interferon stimulates transcription by converting the positive transcriptional regulator ISGF3 from a latent to an active form. - term: id: GO:0070721 label: ISGF3 complex evidence_type: ISS original_reference_id: file:EQUAS/IRF9/IRF9-bioinformatics/human_Q00978-uniprot.txt qualifier: part_of review: summary: IRF9 is the DNA-binding subunit of ISGF3 with STAT1 and STAT2. action: NEW reason: The donkey GOA record has no complex annotation. ISGF3 membership is the defining context of IRF9 activity; IRF9 is itself a structural subunit of the complex, not a substrate or regulator of it. Human IRF9-deficient cells cannot form ISGF3, the donkey protein is in the IRF9 PANTHER subfamily, and it retains the IRF-association domain (Pfam IRF-3) that binds STAT2. supported_by: - reference_id: PMID:30143481 supporting_text: Her cells activate gamma-activated factor (GAF) STAT1 homodimers but not IFN-stimulated gene factor 3 (ISGF3) trimers (STAT1/STAT2/IRF9) in response to IFN-α2b. - reference_id: PMID:1630447 supporting_text: ISGF3 has two components, termed ISGF3 alpha and ISGF3 gamma. - reference_id: file:EQUAS/IRF9/IRF9-uniprot.txt record_section: ["DR:PANTHER"] supporting_text: PTHR11949:SF26; INTERFERON REGULATORY FACTOR 9 references: - id: GO_REF:0000104 title: Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features findings: [] - id: GO_REF:0000117 title: Electronic Gene Ontology annotations created by ARBA machine learning models findings: [] - id: GO_REF:0000118 title: TreeGrafter-generated GO annotations findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: PMID:1630447 title: Subunit of an alpha-interferon-responsive transcription factor is related to interferon regulatory factor and Myb families of DNA-binding proteins. findings: - statement: ISGF3-gamma (IRF9) is the DNA-recognition subunit of ISGF3 and binds DNA sequence-specifically when translated in vitro. supporting_text: ISGF3 gamma serves as the DNA recognition subunit reference_review: relevance: HIGH correctness: VERIFIED review_notes: Cloning of human ISGF3-gamma/p48 (IRF9); cited in the human Swiss-Prot record. Abstract-only in cache; quotes taken from the abstract. - id: PMID:30143481 title: Life-threatening influenza pneumonitis in a child with inherited IRF9 deficiency. findings: - statement: Human IRF9 loss of function abolishes ISGF3 formation, ISRE binding and ISRE-driven transcription in response to IFN-alpha2b, and is rescued by wild-type IRF9. supporting_text: These phenotypes are rescued by wild-type IRF9 reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text cached. Human IRF9 deficiency; EMSA, reporter and fractionation data underpin the DNA-binding, transcription factor, nucleus and ISGF3 rows transferred to donkey within PTHR11949:SF26. - id: PMID:11846981 title: Nuclear/cytoplasmic localization of IRFs in response to viral infection or interferon stimulation. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Review (abstract only) on IRF3 and IRF9 nucleocytoplasmic redistribution; supports the nucleus row. - id: PMID:30826365 title: Impaired control of multiple viral infections in a family with complete IRF9 deficiency. findings: [] reference_review: relevance: LOW correctness: UNVERIFIED review_notes: Second human IRF9-deficiency family, cited by the human Swiss-Prot record for IMD65. Cache has no abstract text, so it is not used as support. - id: file:EQUAS/IRF9/IRF9-uniprot.txt title: UniProt record for donkey IRF9 (A0A9L0I7X9) findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Used for PANTHER subfamily placement (PTHR11949:SF26) and domain content; its ARBA-derived function text is not used as evidence. - id: file:EQUAS/IRF9/IRF9-bioinformatics/human_Q00978-uniprot.txt title: UniProt Swiss-Prot record for human IRF9 (Q00978) findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Human ortholog record in the same PANTHER subfamily. In the 2026-10-21 re-review, quotes of its DR GO lines were replaced by quotes of the primary papers; it is retained for the curated FUNCTION text (ECO:0000269, PMID:30143481). - id: file:EQUAS/IRF9/IRF9-bioinformatics/RESULTS.md title: 'IRF9: donkey-human sequence comparison' findings: - statement: Donkey IRF9 is 80% identical to human over 388 paired residues and has a C-terminal extension. supporting_text: The donkey sequence A0A9L0I7X9 (421 residues) aligns to human Q00978 (393 residues) with 80.41% identity across 388 paired residues. - id: file:EQUAS/IRF9/IRF9-bioinformatics/dbd_check.md title: IRF9 DNA-binding domain check findings: - statement: The IRF DNA-binding domain is 91% identical and all five pentad tryptophans are conserved. supporting_text: '98 of 108 residues identical in donkey A0A9L0I7X9.' core_functions: - description: Sequence-specific DNA-binding subunit of ISGF3 that binds ISRE elements and, with STAT1/STAT2, activates RNA polymerase II transcription of interferon-stimulated genes in response to type I interferon. molecular_function: id: GO:0000981 label: DNA-binding transcription factor activity, RNA polymerase II-specific directly_involved_in: - id: GO:0060337 label: type I interferon-mediated signaling pathway - id: GO:0045944 label: positive regulation of transcription by RNA polymerase II locations: - id: GO:0005634 label: nucleus in_complex: id: GO:0070721 label: ISGF3 complex supported_by: - reference_id: PMID:1630447 supporting_text: ISGF3 gamma serves as the DNA recognition subunit - reference_id: PMID:30143481 supporting_text: Her cells activate gamma-activated factor (GAF) STAT1 homodimers but not IFN-stimulated gene factor 3 (ISGF3) trimers (STAT1/STAT2/IRF9) in response to IFN-α2b. - reference_id: file:EQUAS/IRF9/IRF9-uniprot.txt record_section: ["DR:PANTHER"] supporting_text: PTHR11949:SF26; INTERFERON REGULATORY FACTOR 9 - reference_id: file:EQUAS/IRF9/IRF9-bioinformatics/dbd_check.md supporting_text: '98 of 108 residues identical in donkey A0A9L0I7X9.' suggested_questions: - question: Is the 33-residue C-terminal extension of donkey IRF9 encoded by an expressed exon, and does it affect STAT2 binding by the adjacent IRF-association domain? suggested_experiments: - description: Interferon-alpha stimulation of donkey fibroblasts with ISRE-reporter and STAT2 co-immunoprecipitation assays, comparing endogenous IRF9 with a construct lacking the C-terminal extension.